Merge pull request #67 from Erastova-group/siminp_fixes

Add new tutorial files

Tutorial/builder/IMt-1.yaml

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+
+# =============================================================================
+# General specifications for clay model construction
+# =============================================================================
+
+# =============================================================================
+# Required Parameters
+# =============================================================================
+
+OUTPATH: IMt-1
+
+# name of system to call according to CLAY_COMP (exp_clay.csv)
+# compositions currently included are: 'NAu-1-fe' 'NAu-2-fe' 'NG-1'  'SWa-1' 'L31' 'IMt-1' 'KGa-1'
+SYSNAME: IMt-1
+
+# specify whether new clay model should be constructed:
+# new - a new clay model is constructed
+# load - sheet coordinates or unit cell sequences are loaded from existent ._gro or .npy files
+# load: [X, Y]
+# with X - 'np' or '_gro', Y - '.npy' or '._gro' filename
+# False - no clay model is constructed
+BUILD: new
+
+# name of .csv file with target stoichiometry
+#CLAY_COMP: ./exp_clay.csv
+
+# clay type available options in 'clay_units' directory:
+# clay type available options in 'clay_units' directory:
+# Dioctahedral 2:1 - D21
+# Trioctahedral 2:1 - T21
+# Dioctahedral 1:1 - D11
+# Trioctahedral 1:1 - T11
+# layered double hydroxide 3:1 - L31
+# layered double hydroxide 2:1 - L21
+# Sepiolite - SEP
+
+CLAY_TYPE: CD21
+
+
+# =============================================================================
+# Optional: Clay Sheet and Interlayer Specifications
+# =============================================================================
+
+# number of unit cells in x direction (Default 7)
+X_CELLS: 7
+
+# number of unit cells in y direction (Default 5)
+Y_CELLS: 5
+
+# number of unit cells in z direction (Default 3)
+N_SHEETS: 3
+
+# ----------------------------------------------------------------------------
+# Optional: Unit Cell Composition and Ratios input
+# if not given, these will be calculated from data in the CLAY_COMP .csv file
+# (Default UC_INDEX_LIST: [], UC_RATIOS_LIST: [])
+# -----------------------------------------------------------------------------
+
+# required UCs to builder system as list
+# UC_INDEX_LIST: [1]
+
+# probability list of unit cells in system
+# p(tot): 1.00
+# UC_RATIOS_LIST: [1]
+
+# -----------------------------------------------------------------------------
+
+# interlayer solvent present or not (Default True)
+IL_SOLV: False
+
+# -----------------------------------------------------------------------------
+# Optional: Interlayer Ion Specification Options (comment the other options!)
+# (Default UC_WATERS: 20)
+# -----------------------------------------------------------------------------
+
+# 1. Number of water molecules that should be added per ion (ION_WATERS)
+# a. as ion species dictionary for hydration number
+# ION_WATERS: {'Ca': 12,
+#               'Na': 12
+#               }
+
+# b. as ion species int for hydration number
+# ION_WATERS: 12
+
+# 3. OR per unit cell
+# UC_WATERS: 20
+
+# 4. OR for a target d-spacing value in A
+# SPACING_WATERS: 10.0
+
+# =============================================================================
+# Optional: Simulation Box Specifications
+# =============================================================================
+
+# full simulation box height in A (Default 150.0)
+BOX_HEIGHT: 30 # 150.0
+
+# =============================================================================
+# Optional: Solvation and Bulk Ions Specifications
+# =============================================================================
+
+# Bulk solvent added or not (Default: True)
+BULK_SOLV: false
+
+# Ion species and concentration in mol/L name to add in bulk solvent
+# (Default: BULK_IONS:
+#  Na: 0.1)
+
+BULK_IONS:
+  Na: 0.1
+  Cl: 0.05
+
+# =============================================================================
+# Optional: Simulation Runs Specifications
+# =============================================================================
+
+# -----------------------------------------------------------------------------
+# bash alias for used GROMACS version
+# -----------------------------------------------------------------------------
+
+GMX: gmx 

Tutorial/builder/KGa-1.yaml

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+
+# =============================================================================
+# General specifications for clay model construction
+# =============================================================================
+
+# =============================================================================
+# Required Parameters
+# =============================================================================
+
+OUTPATH: KGa-1
+
+# name of system to call according to CLAY_COMP (exp_clay.csv)
+# compositions currently included are: 'NAu-1-fe' 'NAu-2-fe' 'NG-1'  'SWa-1' 'L31' 'IMt-1' 'KGa-1'
+SYSNAME: KGa-1
+
+# specify whether new clay model should be constructed:
+# new - a new clay model is constructed
+# load - sheet coordinates or unit cell sequences are loaded from existent ._gro or .npy files
+# load: [X, Y]
+# with X - 'np' or '_gro', Y - '.npy' or '._gro' filename
+# False - no clay model is constructed
+BUILD: new
+
+# name of .csv file with target stoichiometry
+CLAY_COMP: ./exp_clay.csv
+
+# clay type available options in 'clay_units' directory:
+# clay type available options in 'clay_units' directory:
+# Dioctahedral 2:1 - D21
+# Trioctahedral 2:1 - T21
+# Dioctahedral 1:1 - D11
+# Trioctahedral 1:1 - T11
+# layered double hydroxide 3:1 - L31
+# layered double hydroxide 2:1 - L21
+# Sepiolite - SEP
+
+CLAY_TYPE: CD11
+
+
+# =============================================================================
+# Optional: Clay Sheet and Interlayer Specifications
+# =============================================================================
+
+# number of unit cells in x direction (Default 7)
+X_CELLS: 7
+
+# number of unit cells in y direction (Default 5)
+Y_CELLS: 5
+
+# number of unit cells in z direction (Default 3)
+N_SHEETS: 3
+
+# ----------------------------------------------------------------------------
+# Optional: Unit Cell Composition and Ratios input
+# if not given, these will be calculated from data in the CLAY_COMP .csv file
+# (Default UC_INDEX_LIST: [], UC_RATIOS_LIST: [])
+# -----------------------------------------------------------------------------
+
+# required UCs to builder system as list
+# UC_INDEX_LIST: [1]
+
+# probability list of unit cells in system
+# p(tot): 1.00
+# UC_RATIOS_LIST: [1]
+
+# -----------------------------------------------------------------------------
+
+# interlayer solvent present or not (Default True)
+IL_SOLV: False  
+
+# -----------------------------------------------------------------------------
+# Optional: Interlayer Ion Specification Options (comment the other options!)
+# (Default UC_WATERS: 20)
+# -----------------------------------------------------------------------------
+
+# 1. Number of water molecules that should be added per ion (ION_WATERS)
+# a. as ion species dictionary for hydration number
+# ION_WATERS: {'Ca': 12,
+#               'Na': 12
+#               }
+
+# b. as ion species int for hydration number
+# ION_WATERS: 12
+
+# 3. OR per unit cell
+UC_WATERS: 0
+
+# 4. OR for a target d-spacing value in A
+# SPACING_WATERS: 10.0
+
+# =============================================================================
+# Optional: Simulation Box Specifications
+# =============================================================================
+
+# full simulation box height in A (Default 150.0)
+BOX_HEIGHT: 150.0
+
+# =============================================================================
+# Optional: Solvation and Bulk Ions Specifications
+# =============================================================================
+
+# Bulk solvent added or not (Default: True)
+BULK_SOLV: True
+
+# Ion species and concentration in mol/L name to add in bulk solvent
+# (Default: BULK_IONS:
+#  Na: 0.1)
+
+BULK_IONS:
+  Na: 0.5
+  Cl: 0.5
+
+# =============================================================================
+# Optional: Simulation Runs Specifications
+# =============================================================================
+
+# -----------------------------------------------------------------------------
+# bash alias for used GROMACS version
+# -----------------------------------------------------------------------------
+
+GMX: gmx

Tutorial/builder/NAu-1.yaml

@@ -0,0 +1,120 @@
+
+# =============================================================================
+# General specifications for clay model construction
+# =============================================================================
+
+# =============================================================================
+# Required Parameters
+# =============================================================================
+
+OUTPATH: 'NAu-1-fe'
+
+# name of system to call according to CLAY_COMP (exp_clay.csv)
+# compositions included are: 'NAu-1-fe' 'NAu-2-fe' 'NG-1'  'SWa-1' 'L31' 'IMt-1' 'KGa-1'
+SYSNAME: NAu-1-fe
+
+# specify whether new clay model should be constructed:
+# new - a new clay model is constructed
+# load - sheet coordinates or unit cell sequences are loaded from existent ._gro or .npy files
+# load: [X, Y]
+# with X - 'np' or '_gro', Y - '.npy' or '._gro' filename
+# False - no clay model is constructed
+BUILD: new
+
+# name of .csv file with target stoichiometry
+CLAY_COMP: ./exp_clay.csv
+
+# clay type available options in 'clay_units' directory:
+# clay type available options in 'clay_units' directory:
+# Dioctahedral 2:1 - D21
+# Trioctahedral 2:1 - T21
+# Dioctahedral 1:1 - D11
+# Trioctahedral 1:1 - T11
+# layered double hydroxide 3:1 - L31
+# layered double hydroxide 2:1 - L21
+# Sepiolite - SEP
+
+CLAY_TYPE: TD21
+
+
+# =============================================================================
+# Optional: Clay Sheet and Interlayer Specifications
+# =============================================================================
+
+# number of unit cells in x direction (Default 7)
+X_CELLS: 7
+
+# number of unit cells in y direction (Default 5)
+Y_CELLS: 5
+
+# number of unit cells in z direction (Default 3)
+N_SHEETS: 3
+
+# ----------------------------------------------------------------------------
+# Optional: Unit Cell Composition and Ratios input
+# if not given, these will be calculated from data in the CLAY_COMP .csv file
+# (Default UC_INDEX_LIST: [], UC_RATIOS_LIST: [])
+# -----------------------------------------------------------------------------
+
+# required UCs to builder system as list
+# UC_INDEX_LIST: [1]
+
+# probability list of unit cells in system
+# p(tot): 1.00
+# UC_RATIOS_LIST: [1]
+
+# -----------------------------------------------------------------------------
+
+# interlayer solvent present or not (Default True)
+IL_SOLV: True
+
+# -----------------------------------------------------------------------------
+# Optional: Interlayer Ion Specification Options (comment the other options!)
+# (Default UC_WATERS: 20)
+# -----------------------------------------------------------------------------
+
+# 1. Number of water molecules that should be added per ion (ION_WATERS)
+# a. as ion species dictionary for hydration number
+# ION_WATERS: {'Ca': 12,
+#               'Na': 12
+#               }
+
+# b. as ion species int for hydration number
+# ION_WATERS: 12
+
+# 3. OR per unit cell
+UC_WATERS: 20
+
+# 4. OR for a target d-spacing value in A
+# SPACING_WATERS: 10.0
+
+# =============================================================================
+# Optional: Simulation Box Specifications
+# =============================================================================
+
+# full simulation box height in A (Default 150.0)
+BOX_HEIGHT: 150.0
+
+# =============================================================================
+# Optional: Solvation and Bulk Ions Specifications
+# =============================================================================
+
+# Bulk solvent added or not (Default: True)
+BULK_SOLV: True
+
+# Ion species and concentration in mol/L name to add in bulk solvent
+# (Default: BULK_IONS:
+#  Na: 0.1)
+
+BULK_IONS:
+  Ca: 0.25
+
+# =============================================================================
+# Optional: Simulation Runs Specifications
+# =============================================================================
+
+# -----------------------------------------------------------------------------
+# bash alias for used GROMACS version
+# -----------------------------------------------------------------------------
+
+GMX: gmx